# System crash on running minimzation on dimer solvated in water **URL:** \ **Category:** User discussions\ **Tags:** mdrun, simulation-setup\ **Created:** [January 13, 2024, 12:07pm UTC](https://gromacs.bioexcel.eu/t/system-crash-on-running-minimzation-on-dimer-solvated-in-water/8032 "2024-01-13T12:07:38Z")\ **Posts on this page:** 2\ **Page:** 1
**Author:** ![meenakshitellis](https://avatars.discourse-cdn.com/v4/letter/m/13edae/32.png) [@meenakshitellis](https://gromacs.bioexcel.eu/u/meenakshitellis)\ **Post date:** [January 13, 2024, 12:07pm UTC](https://gromacs.bioexcel.eu/t/system-crash-on-running-minimzation-on-dimer-solvated-in-water/8032/1 "2024-01-13T12:07:38Z")
GROMACS version: 2021.4-Ubuntu-2021.4-2 GROMACS modification: Yes/No Here post your question Hello, I want to perform REMD simulations on a protein dimer (253aa each) placed at a distance of solvated in different concentrations of urea. For this, first to create only water system I have created box and solvated in water. When I was running energy minimization, the system got crashed and got below error. The two monomers are placed at a distance of 5 angstroms from each other in the system. I prepared the initial configuration as mentioned in attached image from paper “Methods Mol Biol. 2018 ; 1777: 101–119. doi:10.1007/978-1-4939-7811-3\_5. ‘Replica Exchange Molecular Dynamics: A Practical Application Protocol with Solutions to Common Problems and a Peptide Aggregation and Self-Assembly Example’ Ruxi Qi1, Guanghong Wei2, Buyong Ma3, and Ruth Nussinov4,5.” Uploading: Screenshot from 2024-01-13 17-34-08.png… GROMACS: gmx mdrun, version 2021.4-Ubuntu-2021.4-2 Executable: /usr/bin/gmx Data prefix: /usr Working dir: /home/ubuntu/Meenakshi/REMD-simulations/bcn-water Command line: gmx mdrun -v -deffnm em Compiled SIMD: SSE4.1, but for this host/run AVX\_512 might be better (see log). Reading file em.tpr, VERSION 2021.4-Ubuntu-2021.4-2 (single precision) Using 1 MPI thread Using 16 OpenMP threads Steepest Descents: Tolerance (Fmax) = 1.00000e+03 Number of steps = 50000 WARNING: Listed nonbonded interaction between particles 3910 and 3918 at distance 2.751 which is larger than the table limit 2.000 nm. This is likely either a 1,4 interaction, or a listed interaction inside a smaller molecule you are decoupling during a free energy calculation. Since interactions at distances beyond the table cannot be computed, they are skipped until they are inside the table limit again. You will only see this message once, even if it occurs for several interactions. IMPORTANT: This should not happen in a stable simulation, so there is probably something wrong with your system. Only change the table-extension distance in the mdp file if you are really sure that is the reason. Step= 0, Dmax= 1.0e-02 nm, Epot= 1.27151e+33 Fmax= inf, atom= 4719 Segmentation fault (core dumped) What can this be due to? How can I resolve it? ---
**Author:** ![jalemkul](https://dub1.discourse-cdn.com/flex017/user_avatar/gromacs.bioexcel.eu/jalemkul/32/18_2.png) [@jalemkul](https://gromacs.bioexcel.eu/u/jalemkul)\ **Post date:** [January 13, 2024, 1:04pm UTC](https://gromacs.bioexcel.eu/t/system-crash-on-running-minimzation-on-dimer-solvated-in-water/8032/2 "2024-01-13T13:04:10Z")
> [@meenakshitellis](#): > > WARNING: Listed nonbonded interaction between particles 3910 and 3918 > at distance 2.751 which is larger than the table limit 2.000 nm. This warning suggests a problem with the coordinates. What are these atoms? Are their coordinates sensible? Usually this warning is issued when atoms involved in 1-4 interactions are far apart. 2.751 nm would be a very distorted geometry. The magnitude of the force printed by `mdrun` suggests something catastrophically wrong with the coordinates, such that there are overlaps or badly distorted geometries. Check for warnings about long or short bonds from `pdb2gmx` and visualize the structure to make sure it is sensible.